org.jmol.jvxl.readers
Class MapFileReader

java.lang.Object
  org.jmol.jvxl.readers.SurfaceReader
      org.jmol.jvxl.readers.SurfaceFileReader
          org.jmol.jvxl.readers.VolumeFileReader
              org.jmol.jvxl.readers.MapFileReader

All Implemented Interfaces:

VertexDataServer

Direct Known Subclasses:

Dsn6BinaryReader, MrcBinaryReader, XplorReader

abstract class MapFileReader
extends VolumeFileReader

Field Summary

protected float	a
protected Point3f	adjustment
protected float	alpha
protected float	b
protected float	beta
protected float	c
protected float	dmax
protected float	dmean
protected float	dmin
protected float	drange
protected float	gamma
protected int	mapc
protected int	mapr
protected int	maps
protected int	mode
protected int	na
protected int	nb
protected int	nc
protected int	nx
protected int[]	nxyzStart
protected int	ny
protected int	nz
protected Point3f	origin
protected Point3f[]	vectors

Fields inherited from class org.jmol.jvxl.readers.VolumeFileReader

atomCount, boundingBox, canDownsample, downsampleFactor, endOfData, isAngstroms, negativeAtomCount, nSurfaces, readerClosed, thePlane

Fields inherited from class org.jmol.jvxl.readers.SurfaceFileReader

binarydoc, br, line, next, os

Fields inherited from class org.jmol.jvxl.readers.SurfaceReader

allowSigma, ANGSTROMS_PER_BOHR, anisotropy, center, cJvxlEdgeNaN, colorFractionBase, colorFractionRange, contourVertexCount, dataMax, dataMean, dataMin, defaultCutoff, defaultMappedDataMax, defaultMappedDataMin, eccentricityMatrix, eccentricityMatrixInverse, eccentricityRatio, eccentricityScale, edgeFractionBase, edgeFractionRange, fractionData, hasColorData, haveSurfaceAtoms, isAnisotropic, isEccentric, isJvxl, isProgressive, isQuiet, isXLowToHigh, jvxlColorDataRead, jvxlCutoff, jvxlData, jvxlDataIs2dContour, jvxlDataIsColorDensity, jvxlDataIsColorMapped, jvxlDataIsPrecisionColor, jvxlEdgeDataRead, jvxlFileHeaderBuffer, jvxlNSurfaceInts, jvxlVoxelBitSet, marchingCubes, marchingSquares, meshData, meshDataServer, minMax, nBytes, nDataPoints, nPointsX, nPointsY, nPointsZ, params, ptTemp, qpc, sg, vertexDataOnly, volumeData, volumetricOrigin, volumetricVectors, voxelCounts, voxelData, xyzMax, xyzMin, yzCount, yzPlanes

Constructor Summary

MapFileReader(SurfaceGenerator sg, BufferedReader br)

Method Summary

protected void	getVectorsAndOrigin()
protected void	setCutoffAutomatic()

Methods inherited from class org.jmol.jvxl.readers.VolumeFileReader

checkAtomLine, closeReader, getNextVoxelValue, getPlane, getPlaneProcessed, getSurfacePointAndFraction, getValue, getVoxelBitSet, gotoData, initializeSurfaceData, nextVoxel, readParameters, readSurfaceData, readVolumeData, readVolumeParameters, readVoxelVector, recordData, skipComments, skipData

Methods inherited from class org.jmol.jvxl.readers.SurfaceFileReader

discardTempData, getNextQuotedString, getTokens, parseFloat, parseFloat, parseFloatArray, parseFloatArray, parseInt, parseInt, parseIntNext, readLine, setOutputStream, skipTo

Methods inherited from class org.jmol.jvxl.readers.SurfaceReader

addTriangleCheck, addVertexCopy, applyColorScale, colorIsosurface, createIsosurface, excludeMaximumSet, excludeMinimumSet, finalizeMapping, getColorPhaseIndex, getMinMaxMappedValues, getSurfaceAtomIndex, getSurfacePointIndexAndFraction, getValueAtPoint, gotoAndReadVoxelData, initializeMapping, initializeVolumetricData, initPlanes, jvxlUpdateInfo, newVoxelDataCube, postProcessVertices, readAndSetVolumeParameters, readColorData, resetIsosurface, selectPocket, setBoundingBox, setVectorAnisotropy, setVertexAnisotropy, setVolumeData, setVolumetricAnisotropy, setVolumetricOriginAnisotropy, slabIsosurface, updateSurfaceData, updateTriangles

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

dmin

protected float dmin

dmax

protected float dmax

dmean

protected float dmean

drange

protected float drange

mapc

protected int mapc

mapr

protected int mapr

maps

protected int maps

nx

protected int nx

ny

protected int ny

nz

protected int nz

mode

protected int mode

nxyzStart

protected int[] nxyzStart

na

protected int na

nb

protected int nb

nc

protected int nc

a

protected float a

b

protected float b

c

protected float c

alpha

protected float alpha

beta

protected float beta

gamma

protected float gamma

origin

protected Point3f origin

adjustment

protected Point3f adjustment

vectors

protected Point3f[] vectors

Constructor Detail

MapFileReader

MapFileReader(SurfaceGenerator sg,
              BufferedReader br)

Method Detail

getVectorsAndOrigin

protected void getVectorsAndOrigin()

setCutoffAutomatic

protected void setCutoffAutomatic()